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Change VariantEval to not require the output file to already exist. #5681

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merged 2 commits into from
Feb 19, 2019
Merged

Change VariantEval to not require the output file to already exist. #5681

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2b55936
Change VariantEval to not require the output file to already exist.
cmnbroad Feb 14, 2019
39aef2d
Code review comments.
cmnbroad Feb 15, 2019
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1 change: 0 additions & 1 deletion src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval.java
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Original file line number Diff line number Diff line change
Expand Up @@ -306,7 +306,6 @@ protected void initializeDrivingVariants() {
@Override
public void onTraversalStart() {
Utils.nonNull(outFile);
IOUtils.assertFileIsReadable(outFile.toPath());
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Can you add at least one test that would have failed without this patch?


// Just list the modules, and exit quickly.
if (LIST) { variantEvalUtils.listModulesAndExit(); }
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29 changes: 29 additions & 0 deletions ...a/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEvalIntegrationTest.java
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Expand Up @@ -3,10 +3,14 @@
import org.broadinstitute.barclay.argparser.CommandLineException;
import org.broadinstitute.hellbender.CommandLineProgramTest;
import org.broadinstitute.hellbender.exceptions.UserException;
import org.broadinstitute.hellbender.testutils.ArgumentsBuilder;
import org.broadinstitute.hellbender.testutils.IntegrationTestSpec;
import org.broadinstitute.hellbender.utils.SimpleInterval;
import org.broadinstitute.hellbender.utils.io.IOUtils;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
Expand Down Expand Up @@ -636,4 +640,29 @@ public void testPrintMissingComp() throws IOException {
spec.executeTest(name, this);

}

@Test
public void testOutputFileCreation() throws IOException {
// duplicate of "testPrintMissingComp", this time without using IntegrationTestSpec in order to force the
// tool to create the output file directly (tests fix for https://github.com/broadinstitute/gatk/issues/5674)

final String testName = "testOutputFileCreation";
final File tmpDir = createTempDir(testName);
final File outputFile = new File(tmpDir, testName + ".txt");

ArgumentsBuilder argBuilder= new ArgumentsBuilder();
argBuilder.addReference(new File(b37_reference_20_21));
argBuilder.addArgument("eval", getTestFilePath("validationReportEval.noGenotypes.vcf"));
argBuilder.addArgument("comp", getTestFilePath("validationReportComp.noGenotypes.vcf"));
argBuilder.addInterval(new SimpleInterval("20"));
argBuilder.addArgument("EV", "PrintMissingComp");
argBuilder.addOutput(outputFile);

runCommandLine(argBuilder);

IntegrationTestSpec.assertEqualTextFiles(
outputFile,
new File(getToolTestDataDir() + "expected/" + "testPrintMissingComp" + ".expected.txt"));
}

}